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H1N1 - Origin & Timeline

H1N1 - Origin & Timeline

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Vol. 14 · Issue 17 · 30 April 2009 ·
Rapid communications
V Trifonov
, H Khiabanian
, B Greenbaum
, R Rabadan (rabadan@dbmi.columbia.edu)
1. Department o Biomedical Inormatics, Center or Computational Biology and Bioinormatics, Columbia UniversityCollege o Physicians and Surgeons, New York, United States2. The Simons Center or Systems Biology, Institute or Advanced Study, Princeton, United States
Preliminary analysis of the genome of the new H1N1
inuenza A virus responsible for the current pandemic indicatesthat all genetic segments are related closest to those of commonswine inuenza viruses.A new H1N1 inuenza A virus has been identied in Mexico,and has spread rapidly to other regions around the world. The WorldHealth Organization in collaboration with many other national andinternational agencies is working efciently to evaluate, diagnoseand implement measures to contain the spread of this virus. Amongthe many efforts is the timely release of the genomic sequencesfrom different viral isolates [1]. This is allowing thousands ofscientists to participate in the endeavour.There have been some questions raised about the origin of thenew strain. Inuenza A is a single stranded RNA virus with eightdifferent segments. When two viruses co-infect the same cell, newviruses can be produced that contain segments from both parentalstrains.By using sequences collected in public databases, we canidentify the closest relatives of the new strain found in Mexico,and construct clusters and phylogenetic trees. Sequence alignmentand similarity, cluster analyses by principal component analysis andphylogenetic tree all point to similar results.Our preliminary analyses show that the closest relatives tothis new strain are found in swine, and occasionally in turkeys.Six segments of the virus are related to swine viruses from NorthAmerica and the other two (NA and M) from swine viruses isolatedin Europe/Asia. The closest clusters (for the HA segment) in theNCBI data base are North America swine inuenza A(H1N2) andH3N2s. The closest relatives of the neuraminidase (NA) gene ofthe new virus, are inuenza A isolates from 1992. As more databecomes accessible, the evolution of this gene could be claried.The North American ancestors are related to the multiplereassortants, H1N2 and H3N2 swine viruses isolated in NorthAmerica since 1998 [2,3]. In particular, the swine H3N2 isolatesfrom 1998 were a triple reassortment of human, swine and avianorigin.Therefore, this preliminary analysis suggests at least two swineancestors to the current H1N1, one of them related to the triplereassortant viruses isolated in North America in 1998. So far, thenew strain has not been reported in pigs. It is not clear if this is dueto insufcient surveillance of the swine population, or if this virushas been generated in a very recent reassortment event.
1. World Health Organization. Viral gene sequences to assist update diagnosticsor swine infuenza A(H1N1). Geneva: WHO; 2009 April 25. Available rom: http://www.who.int/csr/disease/swinefu/swinefu_genesequences_20090425.pd 2. Karasin AI, Schutten MM, Cooper LA, Smith CB, Subbarao K, Anderson GA, etal. Genetic characterization o H3N2 infuenza viruses isolated rom pigs inNorth America, 1977-1999: evidence or wholly human and reassortant virusgenotypes. Virus Res. 2000;68(1):71-85.3. Karasin AI, Landgra J, Swenson S, Erickson G, Goyal S, Woodru M, et al.H1N2: Genetic characterization o H1N2 infuenza A viruses isolated rompigs throughout the United States. J Clin Microbiol. 2002;40(3):1073-9.
This article was published on 30 April 2009.Citation style or this article: Trionov V, Khiabanian H, Greenbaum B, Rabadan R. Theorigin o the recent swine infuenza A(H1N1) virus inecting humans. Euro Surveill.2009;14(17):pii=19193. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19193
© 2009 CFPSH
page 1 of 27
Flu, Grippe, Avian Influenza,Grippe Aviaire, Fowl Plague,Swine Influenza, Hog Flu, Pig Flu, Equine Influenza, Canine Influenza
Last Updated:
January 19, 2009
 Anna Rovid Spickler, DVM, PhD
Influenza viruses are found in a number of species including birds, humans,swine, horses and dogs. In the mammalian species to which they are adapted, theseviruses cause respiratory disease with high morbidity and low mortality rates. Moresevere cases can occur in conjunction with other diseases or debilitation, as well as ininfancy or old age. In wild birds, avian influenza viruses are typically, though notalways, carried asymptomatically.
In poultry, there are two forms of disease. Lowpathogenicity avian influenza (LPAI) viruses generally cause asymptomaticinfections, mild respiratory disease or decreased egg production.
In contrast, highpathogenicity avian influenza (HPAI) viruses cause severe disease that can kill up to90-100% of a poultry flock.
Some avian influenza viruses can also infect mammalsincluding humans. The severity of zoonotic avian influenza varies with the virus.Although many human infections are limited to conjunctivitis or mild respiratorydisease, some viral strains cause severe disease and death.
Generally, avianinfluenza viruses do not spread efficiently in mammals, and infections remain limitedto individual animals or small groups.
However, some viruses can becomeadapted to a new species and cause outbreaks, epidemics or pandemics.
 Currently, the world is experiencing an extensive HPAI outbreak, with noimmediate prospects for complete, worldwide eradication. In 2003, HPAI viruses of the H5N1 subtype appeared in poultry in several nations in Southeast Asia.
Althoughat times this epidemic appeared to be under control, eradication was never complete.The outbreaks continued to smolder and spread, and eventually avian H5N1 virusesreached other parts of Asia, as well as parts of Europe, the Pacific, Africa and theMiddle East.
The H5N1 strains responsible for this epidemic appear to be unusuallyvirulent. As of January 2009, they have been responsible for approximately 390human infections, generally as the result of close contact with poultry; about twothirds of these cases were fatal.
Avian H5N1 viruses have also infected and killedmammals of other species, including tigers, leopards, housecats, palm civets, a dogand a stone marten.
In addition, numerous deaths have been reported in wildbirds, which usually carry avian influenza viruses asymptomatically.
Thereare fears that an avian H5N1 strain could eventually become adapted to humans,resulting in a human pandemic.Other avian influenza viruses can also undergo cross-species transmission. LPAIH9N2 viruses, which have become endemic in poultry in parts of Asia and the MiddleEast, may be of particular concern.
These viruses have caused disease outbreaksin poultry in many countries.
Recently, they were found in pigs with respiratorydisease and fatal paralysis in China.
In addition, H9N2 viruses have infectedhumans.
As of January 2009, human H9N2 infections have been significantly lesssevere than those caused by avian HPAI H5N1 viruses.
Viruses in the family Orthomyxoviridae cause influenza. There are three generaof influenza viruses:
influenzavirus A
influenzavirus B
and i
nfluenzavirus C 
Theseviruses are also called type A, type B and type C influenza viruses.
Influenza A viruses 
Influenza A viruses include the avian, swine, equine and canine influenzaviruses, as well as the human influenza A viruses. Influenza A viruses are classifiedinto subtypes based on two surface antigens, the hemagglutinin (H) andneuraminidase (N) proteins. There are 16 hemagglutinin antigens (H1 to H16) andnine neuraminidase antigens (N1 to N9).
These two proteins are involved in cellattachment and release from cells, and are also major targets for the immuneresponse.
Only limited subtypes are found in each species of mammal.
Influenza A viruses are also classified into strains. Strains of influenza viruses aredescribed by their type, host, place of first isolation, strain number (if any), year of isolation, and antigenic subtype.
[e.g., the prototype strain of the H7N7 subtype of equine influenza virus, first isolated in Czechoslovakia in 1956, is A/eq/Prague/56(H7N7).] For human strains, the host is omitted.
Last Updated: January 2009
© 2009 CFSPH
page 2 of 27
Antigenic shift and drift in influenza A viruses
Influenza A viruses change frequently. Strains evolveas they accumulate point mutations during virusreplication; this process is sometimes called ‘antigenicdrift’.
A more abrupt change can occur during geneticreassortment. Reassortment is possible whenever twodifferent influenza viruses infect a cell simultaneously;when the new viruses (the ‘progeny’) are assembled, theymay contain some genes from one parent virus and somegenes from the other.
Reassortment between differentstrains results in the periodic emergence of novel strains.Reassortment between subtypes can result in theemergence of a new subtype. Reassortment can also occurbetween avian, swine, equine, canine and humaninfluenza A viruses. This type of reassortment can resultin a ‘hybrid’ virus with, for example, both avian andhuman influenza virus proteins.An abrupt change in the subtypes found in a hostspecies is called an ‘antigenic shift.’ Antigenic shifts canresult from three mechanisms: 1) genetic reassortmentbetween subtypes, 2) the direct transfer of a whole virusfrom one host species into another, or 3) the re-emergenceof a virus that was found previously in a species but is nolonger in circulation.
For example, human viruses cancontinue to circulate in pigs and could re-emerge into thehuman population.
Antigenic drift and antigenic shiftsresult in the periodic emergence of novel influenzaviruses. By evading the immune response, these virusescan cause influenza epidemics and pandemics.
Avian influenza viruses
Avian influenza viruses are found in a wide variety of domesticated and wild birds.
They are also isolatedoccasionally from mammals including humans.
Waterfowl (order Anseriformes) and shorebirds(order Charadriiformes) seem to be the natural reservoirsfor the type A influenza viruses, and carry all of theknown subtypes.
The predominant subtypes inwild ducks change periodically.
Most, though not all,infections in wild waterfowl and shorebirds areasymptomatic.
Poultry can be infected by a wide variety of subtypes;some of these viruses cause avian influenza. Avianinfluenza viruses are classified as either high pathogenicityavian influenza (HPAI) viruses or low pathogenicity avianinfluenza (LPAI) viruses, based on the genetic features of the virus and the severity of disease in poultry.
To date,only subtypes that contained H5 or H7 have caused HPAI;subtypes that contained other hemagglutinins have beenfound only in the LPAI form.
H5 and H7 LPAI virusesalso exist, and can evolve into high pathogenicitystrains.
From 1993 to 2000, LPAI subtypes containingH1 to H7 and H9 to H11 were isolated from live birdmarkets in the northeastern U.S.
 Limited information is available on the subtypesfound in other species of birds. Subtypes that have beenfound in ratites include H3N2, H4N2, H4N6, H5N1,H5N2, H5N9, H7N1, H7N3, H9N2, H10N4 andH10N7.
Isolates from cage birds usually containH3 or H4; however, infections with high pathogenicitysubtypes containing H7 or H5 can also occur.
Swine influenza viruses
Swine influenza viruses are found mainly in pigs, butthey have also been found in other species includinghumans.
There is less antigenic drift in swineinfluenza viruses than in human influenza A viruses.
 The most common subtypes currently found in pigs areH1N1, H1N2 and H3N2 ;however, the situation iscomplex, as two or more viruses of each subtype arecirculating in swine populations.
Recently, H3N1influenza viruses have also been isolated from pigs in theU.S. and Korea,
and H2N3 influenza viruses weredetected in pigs in the U.S.
 One H1N1 virus circulating in the U.S. is the‘classical H1N1 swine influenza virus. This virus, the firstinfluenza virus known to have infected pigs, was firstfound in swine populations in 1918.
An ‘avian-like’ H1N1 virus circulates in European and U.S.pigs.
This virus seems to be an avian influenza virusthat was transmitted whole to pigs.
It has, in somelocations, replaced the classical H1N1 virus.
Adifferent ‘avian-like’ H1N1 virus is co-circulating withthe classical H1N1 virus in pigs in Asia.
In addition,H1N1 reassortant viruses consisting of classical swineinfluenza virus genes and a human PB1 polymerase genehave been found in pigs in Canada.
A wholly humanlineage H1N1 virus was recently reported from pigs inChina.
This virus, which was responsible for anoutbreak of acute respiratory illness in a herd inGuangdong, has been designatedA/Swine/Guangdong/96/06 (H1N1).
 In North America, H3N2 viruses first emerged inpigs in the U.S. Midwest.
The viruses found in theU.S. are triple reassortants.
They containhemagglutinin and neuraminidase proteins from a humaninfluenza virus, and internal proteins from the classicalswine influenza virus, an avian influenza virus and ahuman influenza virus.
New triple reassortant H3N2viruses have recently been found in Canada.
Theseviruses resemble the H3N2 viruses isolated in the U.S.,but contain a different neuraminidase gene from a humaninfluenza virus.
They have been isolated from pigs,turkeys and a Canadian swine farmer.
H3N2 viruses arealso found in Europe and Asia, but these viruses seem tobe the result of reassortment between a human H3N2virus, circulating there in pigs since the 1970s, and theH1N1 ‘avian-like’ virus.
The European H3N2 virusescontain human H3 and N2 proteins, and internal proteinsfrom the avian virus.
 The H1N2 virus in the U.S. is a reassortant of theclassical H1N1 swine influenza virus and the triplereassortant H3N2 virus circulating in the U.S.
SomeH1N2 viruses in Canadian pigs contain neuraminidaseand hemagglutinin genes from two different human

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